Project Summary Eye development is governed by complicated networks of gene regulatory elements, but the field has not yet characterized or even identified most of the regulatory sequences involved. This project will use new comparative genomics approaches to reveal hundreds of regulatory regions in the genome crucial to eye development and function. The project first aims to precisely identify chromosomal regions that are conserved in sighted species? genomes but lost or deteriorating in six blind species with regressed eye structures. Those blind species are 3 unrelated species with the common name ?mole?, 2 unrelated ?mole- rats?, and a blind river dolphin. This aim will be achieved using powerful RERconverge software developed in the Clark and Chikina labs that exploits the phenomenon of convergent evolution to discover genomic regions unique to species sharing a trait, in this case, blindness. Top-scoring regions will then be assayed for expression in the eye and other tissues in a zebrafish model of embryonic development using their sequences from mouse. The second aim will determine the functional consequences of sequence evolution in species with regressed eyesight. To this end, sequences from blind species will be contrasted with sequences from their sighted ancestor using experimental characterization of embryonic expression and genome-wide patterns of open chromatin, as well as through recently introduced computational models. By studying the sequence changes in blind species, specific subsequences important for ocular expression will be identified. In the third aim, the project will determine if these new ocular regions are responsible for congenital eye diseases in human patients. Patients for whom no causal mutation was found will be sequenced at thousands of conserved, non-coding regions that surfaced from our evolutionary and functional analyses for eye function. Since causal mutations are not identified in a majority of cases for most eye diseases, associations between disease and these newly discovered ocular regulatory regions would explain this deficit and allow more comprehensive diagnosis in the clinic. Furthermore, eye regulatory regions identified in this project will provide the field of gene therapy with new sequences and expression patterns to design safer and more precise therapies. Thus, this project directly addresses the mission of the National Eye Institute by providing avenues to better diagnosis and treatment of genetic eye diseases.